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Jia Ming, ChangAuthorMagis CCorresponding AuthorBussotti GAuthorDi Tommaso, PAuthorErb, IAuthorEspinosa-Carrasco JAuthorNotredame CAuthor
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T-Coffee: Tree-based consistency objective function for alignment evaluation

Publicated to:Crispr Knock-Ins In Organoids To Track Tumor Cell Subpopulations. 1079 117-129 - 2014-01-01 1079(), DOI: 10.1007/978-1-62703-646-7_7

Authors: Magis, C; Taly, JF; Bussotti, G; Chang, JM; Di Tommaso, P; Erb, I; Espinosa-Carrasco, J; Notredame, C

Affiliations

Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Universitat Pompeu Fabra, Barcelona, Spain. - Author
CRG, Bioinformat Core Facil, Barcelona, Spain - Author
EBI, Cambridge, England - Author
Univ Pompeu Fabra, CRG, Bioinformat & Genom Programme, Barcelona, Spain - Author

Abstract

T-Coffee, for Tree-based consistency objective function for alignment evaluation, is a versatile multiple sequence alignment (MSA) method suitable for aligning virtually any type of biological sequences. T-Coffee provides more than a simple sequence aligner; rather it is a framework in which alternative alignment methods and/or extra information (i.e., structural, evolutionary, or experimental information) can be combined to reach more accurate and more meaningful MSAs. T-Coffee can be used either by running input data via the Web server ( http://tcoffee.crg.cat/apps/tcoffee/index.html ) or by downloading the T-Coffee package. Here, we present how the package can be used in its command line mode to carry out the most common tasks and multiply align proteins, DNA, and RNA sequences. This chapter particularly emphasizes on the description of T-Coffee special flavors also called "modes," designed to address particular biological problems.

Keywords
3d structureDna/rna sequencesHomolog sequencesMsaMultiple sequence alignmentPromoter alignmentProteinProtein sequencesRnaRna secondary structureStructural informationTransmembrane protein

Quality index

Bibliometric impact. Analysis of the contribution and dissemination channel

The work has been published in the journal Crispr Knock-Ins In Organoids To Track Tumor Cell Subpopulations, Q3 Agency Scopus (SJR), its regional focus and specialization in Genetics, give it significant recognition in a specific niche of scientific knowledge at an international level.

From a relative perspective, and based on the normalized impact indicator calculated from World Citations from Scopus Elsevier, it yields a value for the Field-Weighted Citation Impact from the Scopus agency: 1.48, which indicates that, compared to works in the same discipline and in the same year of publication, it ranks as a work cited above average. (source consulted: ESI Nov 14, 2024)

This information is reinforced by other indicators of the same type, which, although dynamic over time and dependent on the set of average global citations at the time of their calculation, consistently position the work at some point among the top 50% most cited in its field:

  • Field Citation Ratio (FCR) from Dimensions: 4.91 (source consulted: Dimensions Apr 2025)

Specifically, and according to different indexing agencies, this work has accumulated citations as of 2025-04-25, the following number of citations:

  • WoS: 51
  • Scopus: 55
  • Europe PMC: 33
  • OpenCitations: 58
Impact and social visibility

From the perspective of influence or social adoption, and based on metrics associated with mentions and interactions provided by agencies specializing in calculating the so-called "Alternative or Social Metrics," we can highlight as of 2025-04-25:

  • The use, from an academic perspective evidenced by the Altmetric agency indicator referring to aggregations made by the personal bibliographic manager Mendeley, gives us a total of: 54.
  • The use of this contribution in bookmarks, code forks, additions to favorite lists for recurrent reading, as well as general views, indicates that someone is using the publication as a basis for their current work. This may be a notable indicator of future more formal and academic citations. This claim is supported by the result of the "Capture" indicator, which yields a total of: 54 (PlumX).

With a more dissemination-oriented intent and targeting more general audiences, we can observe other more global scores such as:

  • The Total Score from Altmetric: 0.5.
  • The number of mentions on the social network X (formerly Twitter): 1 (Altmetric).
Leadership analysis of institutional authors

This work has been carried out with international collaboration, specifically with researchers from: United Kingdom.

There is a significant leadership presence as some of the institution’s authors appear as the first or last signer, detailed as follows: First Author (Magis, CEDRIK) and Last Author (Notredame, Cedric).

the author responsible for correspondence tasks has been Magis, CEDRIK.